The Experts below are selected from a list of 246 Experts worldwide ranked by ideXlab platform
Cornelius Frommel - One of the best experts on this subject based on the ideXlab platform.
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Inverse Sequence similarity of proteins does not imply structural similarity
FEBS Letters, 2003Co-Authors: Stephan Lorenzen, Christoph Gille, Robert Preissner, Cornelius FrommelAbstract:Abstract There is a debate on the folding of proteins with inverted Sequences. Theoretical approaches and experiments give contradictory results. Many proteins in the Protein Data Bank (PDB) show conspicuous Inverse Sequence similarity (ISS) to each other. Here we analyze whether this ISS is related to structural similarity. For the first time, we performed a large scale three-dimensional (3-D) superposition of corresponding Cα atoms of forwardly and Inversely aligned proteins and tested the degree of secondary structure identity between them. Comparing proteins of less than 50% pairwise Sequence identity, only 0.5% of the Inversely aligned pairs had similar folds (99 out of 19 073), whereas about 9% of forwardly aligned proteins in the same score and length range show similar 3-D structures (1731 out of 19 248). This observation strongly supports the view that the inversion of Sequences in almost all cases leads to a different folding property of the protein. Inverted Sequences are thus suitable as protein-like Sequences for control purposes without relations to existing proteins.
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Inverse Sequence similarity in proteins and its relation to the three dimensional fold
FEBS Letters, 1997Co-Authors: R Preisner, A Goede, E Michalski, Cornelius FrommelAbstract:Abstract Nowadays the most successful strategy for the prediction of the tertiary structure of proteins is the homology-based modelling using known structures. A real chance to predict the general fold of a protein arises only in cases with a sufficient Sequence homology (e.g. 27% over 100 residues). In this analysis we examine the phenomenon of Inverse Sequence similarity (ISS) in proteins and its structural meaning. In Sequence data bases we found a lot of examples for ISS up to 34% identity over 204 residues and a surprisingly large number of self-Inverse protein Sequences. By inspection of Inverse similar Sequence pairs with known tertiary structures we observe that Inverse Sequence alignments above the threshold indicating structural similarity generally do not imply comparable folds for both. From our analysis we conclude that the straightforward employment of ISS for protein structure prediction fails even above the known threshold for ‘safe similarity’.
John Kececioglu - One of the best experts on this subject based on the ideXlab platform.
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Inverse Sequence alignment from partial examples
Workshop on Algorithms in Bioinformatics, 2007Co-Authors: John KececiogluAbstract:When aligning biological Sequences, the choice of parameter values for the alignment scoring function is critical. Small changes in gap penalties, for example, can yield radically different alignments. A rigorous way to compute parameter values that are appropriate for biological Sequences is Inverse parametric Sequence alignment. Given a collection of examples of biologically correct alignments, this is the problem of finding parameter values that make the example alignments score close to optimal. We extend prior work on Inverse alignment to partial examples and to an improved model based on minimizing the average error of the examples. Experiments on benchmark biological alignments show we can find parameters that generalize across protein families and that boost the recovery rate for multiple Sequence alignment by up to 25%.
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WABI - Inverse Sequence alignment from partial examples
Lecture Notes in Computer Science, 2007Co-Authors: John KececiogluAbstract:When aligning biological Sequences, the choice of parameter values for the alignment scoring function is critical. Small changes in gap penalties, for example, can yield radically different alignments. A rigorous way to compute parameter values that are appropriate for biological Sequences is Inverse parametric Sequence alignment. Given a collection of examples of biologically correct alignments, this is the problem of finding parameter values that make the example alignments score close to optimal. We extend prior work on Inverse alignment to partial examples and to an improved model based on minimizing the average error of the examples. Experiments on benchmark biological alignments show we can find parameters that generalize across protein families and that boost the recovery rate for multiple Sequence alignment by up to 25%.
R Preisner - One of the best experts on this subject based on the ideXlab platform.
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Inverse Sequence similarity in proteins and its relation to the three dimensional fold
FEBS Letters, 1997Co-Authors: R Preisner, A Goede, E Michalski, Cornelius FrommelAbstract:Abstract Nowadays the most successful strategy for the prediction of the tertiary structure of proteins is the homology-based modelling using known structures. A real chance to predict the general fold of a protein arises only in cases with a sufficient Sequence homology (e.g. 27% over 100 residues). In this analysis we examine the phenomenon of Inverse Sequence similarity (ISS) in proteins and its structural meaning. In Sequence data bases we found a lot of examples for ISS up to 34% identity over 204 residues and a surprisingly large number of self-Inverse protein Sequences. By inspection of Inverse similar Sequence pairs with known tertiary structures we observe that Inverse Sequence alignments above the threshold indicating structural similarity generally do not imply comparable folds for both. From our analysis we conclude that the straightforward employment of ISS for protein structure prediction fails even above the known threshold for ‘safe similarity’.
Stephan Lorenzen - One of the best experts on this subject based on the ideXlab platform.
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Inverse Sequence similarity of proteins does not imply structural similarity
FEBS Letters, 2003Co-Authors: Stephan Lorenzen, Christoph Gille, Robert Preissner, Cornelius FrommelAbstract:Abstract There is a debate on the folding of proteins with inverted Sequences. Theoretical approaches and experiments give contradictory results. Many proteins in the Protein Data Bank (PDB) show conspicuous Inverse Sequence similarity (ISS) to each other. Here we analyze whether this ISS is related to structural similarity. For the first time, we performed a large scale three-dimensional (3-D) superposition of corresponding Cα atoms of forwardly and Inversely aligned proteins and tested the degree of secondary structure identity between them. Comparing proteins of less than 50% pairwise Sequence identity, only 0.5% of the Inversely aligned pairs had similar folds (99 out of 19 073), whereas about 9% of forwardly aligned proteins in the same score and length range show similar 3-D structures (1731 out of 19 248). This observation strongly supports the view that the inversion of Sequences in almost all cases leads to a different folding property of the protein. Inverted Sequences are thus suitable as protein-like Sequences for control purposes without relations to existing proteins.
Jongnan Chen - One of the best experts on this subject based on the ideXlab platform.
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catalytic decomposition of hydrogen peroxide and 4 chlorophenol in the presence of modified activated carbons
Chemosphere, 2003Co-Authors: Hsuhui Huang, Mingchun Lu, Jongnan ChenAbstract:Abstract The objective of this research was to examine the heterogeneous catalytic decomposition of H 2 O 2 and 4-chlorophenol (4-CP) in the presence of activated carbons modified with chemical pretreatments. The decomposition of H 2 O 2 was suppressed significantly by the change of surface properties including the decreased pH pzc modified with oxidizing agent and the reduced active sites occupied by the adsorption of 4-CP. The apparent reaction rate of H 2 O 2 decomposition was dominated by the intrinsic reaction rates on the surface of activated carbon rather than the mass transfer rate of H 2 O 2 to the solid surface. By the detection of chloride ion in suspension, the reduction of 4-CP was not only attributed to the advanced adsorption but also the degradation of 4-CP. The catalytic activity toward 4-CP for the activated carbon followed the Inverse Sequence of the activity toward H 2 O 2 , suggesting that acidic surface functional group could retard the H 2 O 2 loss and reduce the effect of surface scavenging resulting in the increase of the 4-CP degradation efficiency. Few effective radicals were expected to react with 4-CP for the strong effect of surface scavenging, which could explain why the degradation rate of 4-CP observed in this study was so slow and the dechlorination efficiency was independent of the 4-CP concentration in aqueous phase. Results show that the combination of H 2 O 2 and granular activated carbon (GAC) did increase the total removal of 4-CP than that by single GAC adsorption.
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catalytic decomposition of hydrogen peroxide and 2 chlorophenol with iron oxides
Water Research, 2001Co-Authors: Hsuhui Huang, Mingchun Lu, Jongnan ChenAbstract:The aim of this study was to examine the catalyzed decomposition of hydrogen peroxide and 2-chlorophenol (2-CP) in the presence of iron oxides. Granular ferrihydrite, goethite, and hematite were selected as catalysts in this study. 2-CP was used as the model compound because it is a typical toxic compound and has not been investigated in the catalytic decomposition by iron oxides. The catalytic activity for hydrogen peroxide decomposition followed the Sequence: granular ferrihydrite >goethite> hematite. However, hematite exhibited the highest activity in catalyzing 2-CP oxidation. The oxidation efficiency of 2-CP corresponded with the Inverse Sequence of specific area and pHpzc of the iron oxides. The catalytic activity of granular ferrihydrite was affected significantly by the mixing speed and particle size for its large value of Thiele modulus (j) and Damkohler number (Da). The strong diffusion resistance for granular ferrihydrite was attributed either to its microporous structure or to the formation of oxygen in the pores of the iron oxide leading to the unexpected catalytic activity of granular ferrihydrite to hydrogen peroxide and 2-CP. # 2001 Elsevier Science Ltd. All rights reserved
